public static void PrintSpectrumMS2(StreamWriter sr, MSUltraLight theSpectrum, string identification = null, string fileName = null)
{
sr.WriteLine("S\t" + theSpectrum.ScanNumber + "\t" + theSpectrum.ScanNumber + "\t" + theSpectrum.Precursors[0].Item1);
sr.WriteLine("I\tRetTime\t" + theSpectrum.CromatographyRetentionTime);
if (identification != null)
{
sr.WriteLine("I\tPeptide\t" + identification);
}
if (fileName != null)
{
sr.WriteLine("I\tFileName\t" + fileName);
}
foreach (var precursor in theSpectrum.Precursors)
{
sr.WriteLine("Z\t" + precursor.Item2 + "\t" + PatternTools.pTools.DechargeMSPeakToPlus1(precursor.Item1, precursor.Item2));
}
for (int i = 0; i < theSpectrum.Ions.Count; i++)
{
sr.WriteLine(Math.Round(theSpectrum.Ions[i].Item1, 5) + " " + Math.Round(theSpectrum.Ions[i].Item2, 5));
}
}
public static string PrintSpectrum(MSUltraLight theSpectrum)
{
StringBuilder sb = new StringBuilder();
if (theSpectrum.MSLevel > 1)
{
sb.AppendLine("S\t" + theSpectrum.ScanNumber + "\t" + theSpectrum.ScanNumber + "\t" + theSpectrum.Precursors[0].Item1);
}
else
{
sb.AppendLine("S\t" + theSpectrum.ScanNumber + "\t" + theSpectrum.ScanNumber);
}
sb.AppendLine("I\tRetTime\t" + theSpectrum.CromatographyRetentionTime);
sb.AppendLine("I\tInstrumentType\t" + theSpectrum.InstrumentType);
if (theSpectrum.MSLevel > 1)
{
foreach (Tuple <float, short> precursor in theSpectrum.Precursors)
{
sb.AppendLine("Z\t" + precursor.Item2 + "\t" + PatternTools.pTools.DechargeMSPeakToPlus1(precursor.Item1, precursor.Item2));
}
}
for (int i = 0; i < theSpectrum.Ions.Count; i++)
{
sb.AppendLine(Math.Round(theSpectrum.Ions[i].Item1, 5) + " " + Math.Round(theSpectrum.Ions[i].Item2, 5));
}
return(sb.ToString());
}
/// <summary>
/// Method responsible for parsing RAW File.
/// </summary>
/// <param name="fileName"></param>
/// <returns></returns>
public List <MSUltraLight> ParseFile(String rawFile, short fileIndex = -1, int MsnLevel = 2, List <int> ScanNumbers = null, bool toPrint_console = true)
{
if (!File.Exists(rawFile))
{
throw new Exception("ParserUltraLightRAW error:: Unable to find the file " + rawFile);
}
MSFileReaderLib.IXRawfile2 raw = (MSFileReaderLib.IXRawfile2) new MSFileReader_XRawfile();
raw.Open(rawFile);
raw.SetCurrentController(0, 1);
Dictionary <int, double[, ]> ms1s = null;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary <int, double[, ]>();
}
int first_scan_number = -1;
raw.GetFirstSpectrumNumber(ref first_scan_number);
int last_scan_number = -1;
raw.GetLastSpectrumNumber(ref last_scan_number);
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
MSUltraLight[] myTMSArray = new MSUltraLight[last_scan_number + 2];
//We will only retrieve certain scan numbers
if (ScanNumbers == null)
{
ScanNumbers = new List <int>();
for (int scan_number = first_scan_number; scan_number <= last_scan_number + 1; scan_number++)
{
ScanNumbers.Add(scan_number);
}
}
ScanNumbers.Sort();
foreach (int scan_number in ScanNumbers)
{
spectra_processed++;
string scan_filter = null;
raw.GetFilterForScanNum(scan_number, ref scan_filter);
if (String.IsNullOrEmpty(scan_filter))
{
Console.WriteLine("Scan " + scan_number + " is null");
continue;
}
if (MsnLevel == 1)
{
if (!isMS1.IsMatch(scan_filter))
{
if (!isMS1_1.IsMatch(scan_filter))
{
continue;
}
}
}
else if (MsnLevel == 2)
{
if (!isMS2.IsMatch(scan_filter))
{
continue;
}
}
else if (MsnLevel == 3)
{
if (!isMS3.IsMatch(scan_filter))
{
continue;
}
}
string spectrum_id = "controllerType=0 controllerNumber=1 scan=" + scan_number.ToString();
double retention_time = double.NaN;
raw.RTFromScanNum(scan_number, ref retention_time);
double precursor_mz;
double precursor_intensity;
int precursor_scanNumber;
double ionInjectionTime;
int charge;
if (MsnLevel > 1)
{
GetPrecursor(ms1s, raw, scan_number, scan_filter, first_scan_number, out precursor_mz, out precursor_intensity, out precursor_scanNumber);
DeterminePrecursorParams(raw, scan_number, out charge, out ionInjectionTime);
}
else
{
charge = -1;
precursor_mz = -1;
precursor_intensity = -1;
}
double[,] label_data = GetFragmentationData(raw, scan_number, scan_filter);
List <Tuple <float, float> > peaks = new List <Tuple <float, float> >(label_data.GetLength(1));
for (int peak_index = label_data.GetLowerBound(1); peak_index <= label_data.GetUpperBound(1); peak_index++)
{
// Calculate index in list of ions object
int index = peak_index - label_data.GetLowerBound(1);
// Get fragment ion m/z and intensity from RAW file
float mz = (float)label_data[(int)RawLabelDataColumn.MZ, peak_index];
float intensity = (float)label_data[(int)RawLabelDataColumn.Intensity, peak_index];
// Create new ion object
peaks.Add(new Tuple <float, float>(mz, intensity));
}
if (peaks.Count > 0)
{
MSUltraLight ms = new MSUltraLight((float)retention_time,
scan_number,
peaks,
new List <Tuple <float, short> >()
{
new Tuple <float, short>((float)precursor_mz, (short)charge)
},
(float)precursor_intensity,
1, //Instrument type
(short)MsnLevel,
fileIndex);
myTMSArray[scan_number] = ms;
}
lock (progress_lock)
{
int new_progress = (int)((double)spectra_processed / (last_scan_number - first_scan_number + 1) * 100);
if (new_progress > old_progress)
{
old_progress = new_progress;
if (toPrint_console)
{
int currentLineCursor = Console.CursorTop;
Console.SetCursorPosition(0, Console.CursorTop);
Console.Write(" Reading RAW File: " + old_progress + "%");
Console.SetCursorPosition(0, currentLineCursor);
}
else
{
Console.Write(" Reading RAW File: " + old_progress + "%");
}
}
}
}
Console.Write(" Reading RAW File: 100%");
return(myTMSArray.Where(a => a != null).ToList());
}
public static void PrintSpectrum(StreamWriter sw, MSUltraLight theSpectrum)
{
sw.WriteLine(PrintSpectrum(theSpectrum));
}
/// <summary>
/// The result is sorted by scan number
/// </summary>
/// <param name="fileName"></param>
/// <returns></returns>
public static List <MSUltraLight> ParseSpectra(string fileName)
{
FileInfo fi = new FileInfo(fileName);
if (!fi.Exists)
{
throw new Exception("File " + fi.FullName + " not found.");
}
List <MSUltraLight> theSpectra = new List <MSUltraLight>(100);
if (fi.Extension.Equals(".ms2") || fi.Extension.Equals(".ms3"))
{
//The PathCandidates
Regex tabSeparator = new Regex(@"\t");
Regex mzSeparator = new Regex(@"\s+", RegexOptions.Compiled);
Regex isNumber = new Regex(@"^[0-9]", RegexOptions.Compiled);
Regex RegExRetTime = new Regex(@"RetTime");
Regex RegexActivationType = new Regex(@"ActivationType");
Regex RegexInstrumentType = new Regex(@"InstrumentType");
StreamReader sr = new StreamReader(fileName);
List <Tuple <float, float> > ionsTemp = new List <Tuple <float, float> >();
string line;
MSUltraLight ms = new MSUltraLight();
ms.Precursors = new List <Tuple <float, short> >();
while ((line = sr.ReadLine()) != null)
{
if (isNumber.IsMatch(line))
{
string[] cols = mzSeparator.Split(line);
ionsTemp.Add(new Tuple <float, float>(float.Parse(cols[0]), float.Parse(cols[1])));
}
else if (RegExRetTime.IsMatch(line))
{
string[] theStrings2 = tabSeparator.Split(line);
ms.CromatographyRetentionTime = float.Parse(theStrings2[2]);
}
else if (line.StartsWith("Z"))
{
string[] cols = Regex.Split(line, "\t");
ms.Precursors.Add(new Tuple <float, short>((float.Parse(cols[2])), short.Parse(cols[1])));
}
else if (line.StartsWith("S"))
{
//We have a new spectra // scan
ms.UpdateIons(ionsTemp);
if (fi.Extension.Equals(".ms2"))
{
ms.MSLevel = 2;
}
else
{
ms.MSLevel = 3;
}
theSpectra.Add(ms);
//Step 2:Get the new one ready
ms = new MSUltraLight();
ms.Precursors = new List <Tuple <float, short> >();
ionsTemp = new List <Tuple <float, float> >();
string[] cols = tabSeparator.Split(line);
ms.ScanNumber = int.Parse(cols[1]);
ms.FileNameIndex = -1;
}
}
ms.UpdateIons(ionsTemp);
if (fi.Extension.Equals(".ms2"))
{
ms.MSLevel = 2;
}
else
{
ms.MSLevel = 3;
}
theSpectra.Add(ms);
sr.Close();
//Just in case
theSpectra.Sort((a, b) => a.ScanNumber.CompareTo(b.ScanNumber));
theSpectra.RemoveAt(0);
return(theSpectra);
}
else
{
throw new Exception(fi.Extension + " is not an acceptable extendion");
}
}
